Add the ability to convert from/to awkward array

.readthedocs.yml

@@ -16,6 +16,7 @@ python:
         - docs
         - netcdf
         - h5py
+        - awkward
 
 sphinx:
   builder: html

imas/backends/netcdf/ids_tensorizer.py

@@ -262,3 +262,45 @@ def tensorize(self, path, fillvalue):
                 tmp_var[aos_coords + tuple(map(slice, node.shape))] = node.value
 
         return tmp_var
+
+    def _recursively_convert_to_list(
+        self, path: str, inactive_index: Tuple, shape: Tuple, i_dim: int
+    ):
+        entry = []
+        for index in range(shape[i_dim]):
+            new_index = inactive_index + (index,)
+            if i_dim == len(shape) - 1:
+                entry.append(self.filled_data[path][new_index].value)
+            else:
+                entry.append(
+                    self._recursively_convert_to_list(path, new_index, shape, i_dim + 1)
+                )
+        return entry
+
+    def awkward_tensorize(self, path: str):
+        """
+        Tensorizes the data at the given path with the specified fill value.
+
+        Args:
+            path: The path to the data in the IDS.
+
+        Returns:
+            A tensor filled with the data from the specified path.
+        """
+        if not self.filled_data[path]:
+            return []
+        hdf5_dim = len(next(iter(self.filled_data[path])))
+
+        if hdf5_dim == 0:
+            return self.filled_data[path][()].value
+
+        if path in self.shapes:
+            shape = self.shapes[path].shape[:hdf5_dim]
+        else:
+            dimensions = self.ncmeta.get_dimensions(path, self.homogeneous_time)
+            full_shape = tuple(self.dimension_size[dim] for dim in dimensions)
+            # Get the split between HDF5 indices and stored matrices
+            # i.e. equilibrium.time_slice.profiles_2d <-> psi
+            shape = full_shape[:hdf5_dim]
+
+        return self._recursively_convert_to_list(path, tuple(), shape, 0)

imas/test/test_wrangle.py

@@ -0,0 +1,260 @@
+import pytest
+import numpy as np
+
+try:
+    import awkward as ak
+except ImportError as exc:
+    raise ImportError(
+        "awkward-array is required" "Install it with: pip install imas-python[awkward]"
+    ) from exc
+
+from imas.wrangler import wrangle, unwrangle
+from imas.ids_factory import IDSFactory
+from imas.util import idsdiffgen
+
+
+@pytest.fixture
+def test_data():
+    data = {"equilibrium": {}}
+    data["equilibrium"]["N_time"] = 100
+    data["equilibrium"]["N_radial"] = 100
+    data["equilibrium"]["N_grid"] = 1
+    data["equilibrium"]["time"] = np.linspace(0.0, 5.0, data["equilibrium"]["N_time"])
+    data["equilibrium"]["psi_1d"] = np.linspace(
+        0.0, 1.0, data["equilibrium"]["N_radial"]
+    )
+    data["equilibrium"]["r"] = np.linspace(1.0, 2.0, data["equilibrium"]["N_radial"])
+    data["equilibrium"]["z"] = np.linspace(-1.0, 1.0, data["equilibrium"]["N_radial"])
+    r_grid, z_grid = np.meshgrid(
+        data["equilibrium"]["r"], data["equilibrium"]["z"], indexing="ij"
+    )
+    data["equilibrium"]["psi_2d"] = (r_grid - 1.5) ** 2 + z_grid**2
+
+    data["thomson_scattering"] = {}
+    data["thomson_scattering"]["N_ch"] = (20, 10)
+    N = data["thomson_scattering"]["N_ch"][0] + data["thomson_scattering"]["N_ch"][1]
+    data["thomson_scattering"]["identifier"] = np.asarray(
+        "channel_" + np.asarray(np.linspace(1, N + 1, N, dtype=int), dtype="|U2"),
+        dtype="|U10",
+    )
+    data["thomson_scattering"]["N_time"] = (100, 300)
+    data["thomson_scattering"]["r"] = np.concatenate(
+        [
+            np.ones(data["thomson_scattering"]["N_ch"][0]) * 1.6,
+            np.ones(data["thomson_scattering"]["N_ch"][1]) * 1.7,
+        ]
+    )
+    data["thomson_scattering"]["z"] = np.concatenate(
+        [
+            np.linspace(-1.0, 1.0, data["thomson_scattering"]["N_ch"][0]),
+            np.linspace(-1.0, 1.0, data["thomson_scattering"]["N_ch"][1]),
+        ]
+    )
+    data["thomson_scattering"]["t_e"] = data["thomson_scattering"]["z"] ** 2 * 5.0e3
+    data["thomson_scattering"]["n_e"] = data["thomson_scattering"]["z"] ** 2 * 5.0e19
+    data["thomson_scattering"]["time"] = (
+        np.linspace(0, 5.0, data["thomson_scattering"]["N_time"][0]),
+        np.linspace(0, 5.0, data["thomson_scattering"]["N_time"][1]),
+    )
+    return data
+
+
+@pytest.fixture
+def flat(test_data):
+    flat = {}
+    # Equilibrium test data
+    flat["equilibrium.time"] = test_data["equilibrium"]["time"]
+    flat["equilibrium.time_slice.time"] = test_data["equilibrium"]["time"]
+    flat["equilibrium.ids_properties.homogeneous_time"] = 1
+    flat["equilibrium.time_slice.profiles_1d.psi"] = np.zeros(
+        (test_data["equilibrium"]["N_time"], test_data["equilibrium"]["N_radial"])
+    )
+    flat["equilibrium.time_slice.profiles_1d.psi"][:] = test_data["equilibrium"][
+        "psi_1d"
+    ]
+    flat["equilibrium.time_slice.profiles_2d.grid.dim1"] = np.zeros(
+        (
+            test_data["equilibrium"]["N_time"],
+            test_data["equilibrium"]["N_grid"],
+            test_data["equilibrium"]["N_radial"],
+        )
+    )
+    flat["equilibrium.time_slice.profiles_2d.grid.dim1"][:] = test_data["equilibrium"][
+        "r"
+    ][None, :]
+    flat["equilibrium.time_slice.profiles_2d.grid.dim2"] = np.zeros(
+        (
+            test_data["equilibrium"]["N_time"],
+            test_data["equilibrium"]["N_grid"],
+            test_data["equilibrium"]["N_radial"],
+        )
+    )
+    flat["equilibrium.time_slice.profiles_2d.grid.dim2"][:] = test_data["equilibrium"][
+        "z"
+    ][None, :]
+    flat["equilibrium.time_slice.profiles_2d.psi"] = np.zeros(
+        (
+            test_data["equilibrium"]["N_time"],
+            test_data["equilibrium"]["N_grid"],
+            test_data["equilibrium"]["N_radial"],
+            test_data["equilibrium"]["N_radial"],
+        )
+    )
+    flat["equilibrium.time_slice.profiles_2d.psi"][:] = test_data["equilibrium"][
+        "psi_2d"
+    ][None, ...]
+    # Thomson scattering test data (ragged)
+    flat["thomson_scattering.channel.identifier"] = test_data["thomson_scattering"][
+        "identifier"
+    ]
+    flat["thomson_scattering.ids_properties.homogeneous_time"] = 0
+    flat["thomson_scattering.channel.t_e.time"] = ak.concatenate(
+        [
+            np.tile(
+                test_data["thomson_scattering"]["time"][0],
+                (test_data["thomson_scattering"]["N_ch"][0], 1),
+            ),
+            np.tile(
+                test_data["thomson_scattering"]["time"][1],
+                (test_data["thomson_scattering"]["N_ch"][1], 1),
+            ),
+        ]
+    )
+    flat["thomson_scattering.channel.t_e.data"] = ak.concatenate(
+        [
+            np.repeat(
+                test_data["thomson_scattering"]["t_e"][
+                    : test_data["thomson_scattering"]["N_ch"][0], None
+                ],
+                test_data["thomson_scattering"]["N_time"][0],
+                axis=1,
+            ),
+            np.repeat(
+                test_data["thomson_scattering"]["t_e"][
+                    test_data["thomson_scattering"]["N_ch"][0] :, None
+                ],
+                test_data["thomson_scattering"]["N_time"][1],
+                axis=1,
+            ),
+        ]
+    )
+    flat["thomson_scattering.channel.n_e.time"] = ak.concatenate(
+        [
+            np.tile(
+                test_data["thomson_scattering"]["time"][0],
+                (test_data["thomson_scattering"]["N_ch"][0], 1),
+            ),
+            np.tile(
+                test_data["thomson_scattering"]["time"][1],
+                (test_data["thomson_scattering"]["N_ch"][1], 1),
+            ),
+        ]
+    )
+    flat["thomson_scattering.channel.n_e.data"] = ak.concatenate(
+        [
+            np.repeat(
+                test_data["thomson_scattering"]["n_e"][
+                    : test_data["thomson_scattering"]["N_ch"][0], None
+                ],
+                test_data["thomson_scattering"]["N_time"][0],
+                axis=1,
+            ),
+            np.repeat(
+                test_data["thomson_scattering"]["n_e"][
+                    test_data["thomson_scattering"]["N_ch"][0] :, None
+                ],
+                test_data["thomson_scattering"]["N_time"][1],
+                axis=1,
+            ),
+        ]
+    )
+    flat["thomson_scattering.channel.position.r"] = test_data["thomson_scattering"]["r"]
+    flat["thomson_scattering.channel.position.z"] = test_data["thomson_scattering"]["z"]
+    return flat
+
+
+@pytest.fixture
+def test_ids_dict(test_data):
+    factory = IDSFactory("3.41.0")
+    equilibrium = factory.equilibrium()
+    equilibrium.time = test_data["equilibrium"]["time"]
+    equilibrium.time_slice.resize(test_data["equilibrium"]["N_time"])
+    equilibrium.ids_properties.homogeneous_time = 1
+    for i in range(test_data["equilibrium"]["N_time"]):
+        equilibrium.time_slice[i].time = test_data["equilibrium"]["time"][i]
+        equilibrium.time_slice[i].profiles_1d.psi = test_data["equilibrium"]["psi_1d"]
+        equilibrium.time_slice[i].profiles_2d.resize(1)
+        equilibrium.time_slice[i].profiles_2d[0].grid.dim1 = test_data["equilibrium"][
+            "r"
+        ]
+        equilibrium.time_slice[i].profiles_2d[0].grid.dim2 = test_data["equilibrium"][
+            "z"
+        ]
+        equilibrium.time_slice[i].profiles_2d[0].psi = test_data["equilibrium"][
+            "psi_2d"
+        ]
+
+    thomson_scattering = factory.thomson_scattering()
+    thomson_scattering.ids_properties.homogeneous_time = 0
+    N = (
+        test_data["thomson_scattering"]["N_ch"][0]
+        + test_data["thomson_scattering"]["N_ch"][1]
+    )
+    thomson_scattering.channel.resize(N)
+    index = 0
+    for i in range(N):
+        if i == test_data["thomson_scattering"]["N_ch"][0]:
+            index = 1
+        thomson_scattering.channel[i].identifier = test_data["thomson_scattering"][
+            "identifier"
+        ][i]
+        thomson_scattering.channel[i].t_e.time = test_data["thomson_scattering"][
+            "time"
+        ][index]
+        thomson_scattering.channel[i].t_e.data = np.tile(
+            test_data["thomson_scattering"]["t_e"][i],
+            test_data["thomson_scattering"]["N_time"][index],
+        )
+        thomson_scattering.channel[i].n_e.time = test_data["thomson_scattering"][
+            "time"
+        ][index]
+        thomson_scattering.channel[i].n_e.data = np.tile(
+            test_data["thomson_scattering"]["n_e"][i],
+            test_data["thomson_scattering"]["N_time"][index],
+        )
+        thomson_scattering.channel[i].position.r = test_data["thomson_scattering"]["r"][
+            i
+        ]
+        thomson_scattering.channel[i].position.z = test_data["thomson_scattering"]["z"][
+            i
+        ]
+
+    return {"equilibrium": equilibrium, "thomson_scattering": thomson_scattering}
+
+
+def test_wrangle(test_ids_dict, flat):
+    wrangled = wrangle(flat)
+    for key in test_ids_dict:
+        diff = idsdiffgen(wrangled[key], test_ids_dict[key])
+        assert len(list(diff)) == 0, diff
+
+
+def get_dtype(arr):
+    """Get dtype from either numpy or awkward array."""
+    if isinstance(arr, ak.Array):
+        # Easiest way to extract the numpy dtype from an awkward array
+        return eval("np." + arr.typestr.split("*")[-1])
+    if hasattr(arr, "dtype"):
+        return arr.dtype
+    else:
+        return type(arr)
+
+
+def test_unwrangle(test_ids_dict, flat):
+    result, failed = unwrangle(list(flat.keys()), test_ids_dict)
+    assert len(failed) == 0, f"The following fields failed to load {failed}"
+    for key in flat.keys():
+        if np.issubdtype(get_dtype(result[key]), np.floating):
+            assert ak.almost_equal(result[key], flat[key])
+        else:
+            assert ak.array_equal(result[key], flat[key])